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comparison fasta_extract.py @ 3:79167132946d draft

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Uploaded
author greg
date Sun, 10 Jan 2016 13:56:47 -0500
parents 3fb7f36c2c8a
children 99c868b492bb
comparison
equal deleted inserted replaced
2:4dc6890db112 3:79167132946d
43 43
44 for (input_filename, hid) in args.inputs: 44 for (input_filename, hid) in args.inputs:
45 extend_existing = args.extend_existing == 'existing' 45 extend_existing = args.extend_existing == 'existing'
46 consider_strand = args.strand == 'yes' 46 consider_strand = args.strand == 'yes'
47 reader = csv.reader(open(input_filename, 'rU'), delimiter='\t') 47 reader = csv.reader(open(input_filename, 'rU'), delimiter='\t')
48 fasta_output_path = get_output_path(args.hid, 48 fasta_output_path = get_output_path(hid,
49 args.subtract_from_start, 49 args.subtract_from_start,
50 args.add_to_end, 50 args.add_to_end,
51 extend_existing, 51 extend_existing,
52 consider_strand) 52 consider_strand)
53 output = open(fasta_output_path, 'wb') 53 output = open(fasta_output_path, 'wb')
54 gff_output_path = get_output_path(args.hid, 54 gff_output_path = get_output_path(hid,
55 args.subtract_from_start, 55 args.subtract_from_start,
56 args.add_to_end, 56 args.add_to_end,
57 extend_existing, 57 extend_existing,
58 consider_strand, 58 consider_strand,
59 orphan=True) 59 orphan=True)